Kang Jin

kangjin at fas.harvard.edu [Github] [Google Scholar] [Twitter]
Last updated: 12/17/2023

Research Interest

Hi, I am a postdoc in Xiaowei Zhuang Lab in the Department of Chemistry and Chemical Biology at Harvard University. I was a Ph.D. student in Bruce Aronow Lab at Cincinnati Children’s Hospital, and a visiting student in Shu lab at Massachusetts General Hospital.

As an enthusiastic researcher, I am passionate about harnessing advanced computational techniques to unveil the biological mechanisms hidden within high-content imaging and high-throughput sequencing data, with a specific focus on image-based spatial profiling. My previous work primarily centered around the development of cutting-edge deep learning models tailored to image-based spatial omics data (Jin*, Zhang* et al., bioRxiv, 2023) and the analysis of temporal perturbation patterns in single-cell experiments (Jin et al., Briefings in Bioinformatics, 2022). My commitment extends to active involvement in the experimental design of spatial multi-omics experiments, and I possess a wealth of experience in exploring single cell data across various biological systems and diseases, including HLHS (Xu, Jin et al., Cell Stem Cell, 2022), schizophrenia (Sebastian*, Jin* et al. Nat Communications, 2023), among others.

I am particularly interested in cutting-edge bioengineering innovations, such as image-based spatial transcriptomics and optical molecular recording. With expertise in computational biology and a strong interest in bioengineering, my ultimate goal is to advance our understanding of neuroscience and cancer biology by implementing cutting-edge computational methods with emerging new molecular recording technologies.

Position & Education

2023 - Present, Depart of Chemistry and Chemical Biology, Harvard University,


2022 - 2023, Massachusetts General Hospital, Harvard Medical School,

Visiting student

2018 - 2023, Department of Biomedical Informatics, Cincinnati Children's Hospital, University of Cincinnati,

Ph.D. student

2014 - 2018, Department of Life Sciences, Zhejiang University,

Bachelor of Biological Science


(*Equal contribution)
Published papers (as main author)
  • Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings [paper] [code]
    Kang Jin*, Zuobai Zhang*, Ke Zhang, Francesca Viggiani, Claire Callahan, Jian Tang, Bruce J. Aronow, Jian Shu
    bioRxiv (2023).

  • CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data [paper] [code]
    Kang Jin, Dan Schnell, Guangyuan Li, Nathan Salomonis, Surya Prasath, Rhonda Szczesniak, Bruce J Aronow
    Briefings in Bioinformatics (2022).

  • Single cell transcriptomic profiling of human brain organoids reveals developmental timing- and cell-type-specific vulnerabilities induced by NRXN1 CNVs in schizophrenia [paper] [code]
    Rebecca Sebastian*, Kang Jin*, Narciso Pavon, Ruby Bansal, Andrew Potter, Yoonjae Song, Juliana Babu, Rafael Gabriel, Yubing Sun, Bruce Aronow, ChangHui Pak
    Nature Communications (2023).

  • An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses [paper] [code]
    Kang Jin, Eric E. Bardes, Alexis Mitelpunkt, Jake Y. Wang, Surbhi Bhatnagar, Soma Sengupta, Daniel Pomeranz Krummel, Marc E. Rothenberg, Bruce J. Aronow
    iScience (2021).

  • Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease [paper]
    Xinxiu Xu, Kang Jin, Abha S Bais, Wenjuan Zhu, Hisato Yagi, Timothy N Feinstein, Phong K Nguyen, Joseph D Criscione, Xiaoqin Liu, Gisela Beutner, Kalyani B Karunakaran, Krithika S Rao, Haoting He, Phillip Adams, Catherine K Kuo, Dennis Kostka, Gloria S Pryhuber, Sruti Shiva, Madhavi K Ganapathiraju, George A Porter Jr, Jiuann-Huey Ivy Lin, Bruce Aronow, Cecilia W Lo
    Cell Stem Cell (2022).

  • Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma [paper] [code]
    Alexander Bondoc*, Kathryn Glaser*, Kang Jin*, Charissa Lake, Stefano Cairo, James Geller, Gregory Tiao, Bruce Aronow
    Communications Biology (2021).

Published papers (as contributing author)
  • Guided construction of single cell reference for human and mouse lung [paper]
    Minzhe Guo, Michael P Morley, Yixin Wu, Yina Du, Shuyang Zhao, Andrew Wagner, Michal Kouril, Kang Jin, ..., Yan Xu
    Nature Communications (2023).

  • KAT5 activity regulates G0-like states in human gliomas [paper]
    Anca B. Mihalas, Sonali Arora, Samantha A. O’Connor, Heather M. Feldman, John Bassett, Kelly Mitchell, Kang Jin, ..., Patrick J. Paddisons
    bioRxiv (2022).

  • LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung [paper]
    Nathan Gaddis, Joshua Fortriede, Minzhe Guo, ..., Kang Jin, ..., Nathan Salomonis, NHLBI LungMAP Consortium
    American Journal of Respiratory Cell and Molecular Biology (2022).

  • Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons [paper]
    Danny McSweeney, Rafael Gabriel, Kang Jin, Zhiping P Pang, Bruce J Aronow, ChangHui Pak
    iScience (2022).

  • A census of the lung: CellCards from LungMAP [paper]
    Xin Sun, Anne-Karina Perl, Rongbo Li, ..., Kang Jin, ..., Edward E Morrisey, NHLBI LungMAP Consortium
    Developmental Cell (2022).

  • Cross-platform validation of neurotransmitter release impairments in schizophrenia patient-derived NRXN1-mutant neurons [paper]
    ChangHui Pak, Tamas Danko, Vincent R. Mirabella, Jinzhao Wang, Yingfei Liu, Madhuri Vangipuram, Sarah Grieder, Xianglong Zhang, Thomas Ward, Yu-Wen Alvin Huang, Kang Jin, ..., Thomas C. Südhof
    PNAS (2021).

  • Functional immune deficiency syndrome via intestinal infection in COVID-19 [paper]
    Erica T. Prates, Michael R. Garvin, Mirko Pavicic, Piet Jones, Manesh Shah, Christiane Alvarez, David Kainer, Omar Demerdash, B Kirtley Amos, Armin Geiger, John Pestian, Kang Jin, Alexis Mitelpunkt, Eric Bardes, Bruce Aronow, Daniel Jacobson
    bioRxiv (2020).

  • Predicted Arabidopsis interactome resource and gene set linkage analysis: a transcriptomic analysis resource [paper]
    Heng Yao, Xiaoxuan Wang, Pengcheng Chen, Ling Hai, Kang Jin, Lixia Yao, Chuanzao Mao, Xin Chen
    Plant Physiology (2018).


  • Bering: Cell segmentation and annotation in high-resolution spatial transcriptomics data

  • ToppCell: Single-cell gene module exploratory platform

  • CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data.

  • Bering: Gene colocalization-aware segmentation of image-based spatial transcriptomics using deep learning models (Wrapping up)


Honors and Awards

  • Second Place, Best Poster Award, ISMB 2022 (SysMod Meeting) 2022
  • Second Place in Graduate Student Research Forum (GSRF), University of Cincinnati, 2020
  • Best Application Award of Zhejiang Bioinformatics Competition,2017
  • China National Award, 2017
  • First Prize Scholarship for Excellent Students, Zhejiang University, 2017
  • Tang Lixin Scholarship for Excellent Model Student, 2017
  • Zhejiang Provincial Government Scholarship, 2016
  • Second Prize, Physics Innovation Competition in Zhejiang Province, 2015